Mechanochemical ATPases and transcriptional activation

Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5

Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.

OrpR is a σ54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough

Enhancer binding proteins (EBPs) are key players of σ⁵⁴ -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ⁵⁴ -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]²⁺ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ⁵⁴ -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.

Tetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR

The Pseudomonas putida phenol-responsive regulator DmpR is a bacterial enhancer binding protein (bEBP) from the AAA⁺ ATPase family. Even though it was discovered more than two decades ago and has been widely used for aromatic hydrocarbon sensing, the activation mechanism of DmpR has remained elusive. Here, we show that phenol-bound DmpR forms a tetramer composed of two head-to-head dimers in a head-to-tail arrangement. The DmpR-phenol complex exhibits altered conformations within the C-termini of the sensory domains and shows an asymmetric orientation and angle in its coiled-coil linkers. The structural changes within the phenol binding sites and the downstream ATPase domains suggest that the effector binding signal is propagated through the coiled-coil helixes. The tetrameric DmpR-phenol complex interacts with the σ⁵⁴ subunit of RNA polymerase in presence of an ATP analogue, indicating that DmpR-like bEBPs tetramers utilize a mechanistic mode distinct from that of hexameric AAA⁺ ATPases to activate σ⁵⁴-dependent transcription.

Regulation of Burkholderia cenocepacia biofilm formation by RpoN and the c-di-GMP effector BerB

Knowledge about the molecular mechanisms that are involved in the regulation of biofilm formation is essential for the development of biofilm‐control measures. It is well established that the nucleotide second messenger cyclic diguanosine monophosphate (c‐di‐GMP) is a positive regulator of biofilm formation in many bacteria, but more knowledge about c‐di‐GMP effectors is needed. We provide evidence that c‐di‐GMP, the alternative sigma factor RpoN (σ54), and the enhancer‐binding protein BerB play a role in biofilm formation of Burkholderia cenocepacia by regulating the production of a biofilm‐stabilizing exopolysaccharide. Our findings suggest that BerB binds c‐di‐GMP, and activates RpoN‐dependent transcription of the berA gene coding for a c‐di‐GMP‐responsive transcriptional regulator. An increased level of the BerA protein in turn induces the production of biofilm‐stabilizing exopolysaccharide in response to high c‐di‐GMP levels. Our findings imply that the production of biofilm exopolysaccharide in B. cenocepacia is regulated through a cascade involving two consecutive transcription events that are both activated by c‐di‐GMP. This type of regulation may allow tight control of the expenditure of cellular resources.

Mechanism of Antiactivation at the Pseudomonas sp. Strain ADP σN-Dependent PatzT Promoter

PatzT is an internal promoter of the atzRSTUVW operon that directs the synthesis of AtzT, AtzU, AtzV, and AtzW, components of an ABC-type cyanuric acid transport system. PatzT is σ(N) dependent, activated by the general nitrogen control regulator NtrC with the assistance of protein integration host factor (IHF), and repressed by the LysR-type transcriptional regulator (LTTR) AtzR. We have used a variety of in vivo and in vitro gene expression and protein-DNA interaction assays to assess the mechanisms underlying AtzR-dependent repression of PatzT Here, we show that repression only occurs when AtzR and NtrC interact simultaneously with the PatzT promoter region, indicating that AtzR acts as an antiactivator to antagonize activation by NtrC. Furthermore, repression requires precise rotational orientation of the AtzR and NtrC binding sites, strongly suggesting protein-protein interaction between the two proteins on the promoter region. Further exploration of the antiactivation mechanism showed that although AtzR-dependent repression occurs prior to open complex formation, AtzR does not alter the oligomerization state of NtrC or inhibit NtrC ATPase activity when bound to the PatzT promoter region. Taken together, these results strongly suggest that PatzT-bound AtzR interacts with NtrC to prevent the coupling of NtrC-mediated ATP hydrolysis with the remodeling of the interactions between E-σ(N) and PatzT that lead to open complex formation.

IMPORTANCE

Here, we describe a unique mechanism by which the regulatory protein AtzR prevents the activation of the σ(N)-dependent promoter PatzT Promoters of this family are always positively regulated, but there are a few examples of overlapping negative regulation. The mechanism described here is highly unconventional and involves an interaction between the repressor and activator proteins to prevent the action of the repressor protein on the RNA polymerase-promoter complex.

Identification of the HrpS binding site in the hrpL promoter and effect of the RpoN binding site of HrpS on the regulation of the type III secretion system in Erwinia amylovora

The type III secretion system (T3SS) is a key pathogenicity factor in Erwinia amylovora. Previous studies have demonstrated that the T3SS in E. amylovora is transcriptionally regulated by an RpoN-HrpL sigma factor cascade, which is activated by the bacterial alarmone (p)ppGpp. In this study, the binding site of HrpS, an enhancer binding protein, was identified for the first time in plant-pathogenic bacteria. Complementation of the hrpL mutant with promoter deletion constructs of the hrpL gene and promoter activity analyses using various lengths of the hrpL promoter fused to a promoter-less green fluorescent protein (gfp) reporter gene delineated the upstream region for HrpS binding. Sequence analysis revealed a dyad symmetry sequence between -138 and -125 nucleotides (TGCAA-N4-TTGCA) as the potential HrpS binding site, which is conserved in the promoter of the hrpL gene among plant enterobacterial pathogens. Results of quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and electrophoresis mobility shift assay coupled with site-directed mutagenesis (SDM) analysis showed that the intact dyad symmetry sequence was essential for HrpS binding, full activation of T3SS gene expression and virulence. In addition, the role of the GAYTGA motif (RpoN binding site) of HrpS in the regulation of T3SS gene expression in E. amylovora was characterized by complementation of the hrpS mutant using mutant variants generated by SDM. Results showed that a Y100F substitution of HrpS complemented the hrpS mutant, whereas Y100A and Y101A substitutions did not. These results suggest that tyrosine (Y) and phenylalanine (F) function interchangeably in the conserved GAYTGA motif of HrpS in E. amylovora.

A model for sigma factor competition in bacterial cells

Sigma factors control global switches of the genetic expression program in bacteria. Different sigma factors compete for binding to a limited pool of RNA polymerase (RNAP) core enzymes, providing a mechanism for cross-talk between genes or gene classes via the sharing of expression machinery. To analyze the contribution of sigma factor competition to global changes in gene expression, we develop a theoretical model that describes binding between sigma factors and core RNAP, transcription, non-specific binding to DNA and the modulation of the availability of the molecular components. The model is validated by comparison with in vitro competition experiments, with which excellent agreement is found. Transcription is affected via the modulation of the concentrations of the different types of holoenzymes, so saturated promoters are only weakly affected by sigma factor competition. However, in case of overlapping promoters or promoters recognized by two types of sigma factors, we find that even saturated promoters are strongly affected. Active transcription effectively lowers the affinity between the sigma factor driving it and the core RNAP, resulting in complex cross-talk effects. Sigma factor competition is not strongly affected by non-specific binding of core RNAPs, sigma factors and holoenzymes to DNA. Finally, we analyze the role of increased core RNAP availability upon the shut-down of ribosomal RNA transcription during the stringent response. We find that passive up-regulation of alternative sigma-dependent transcription is not only possible, but also displays hypersensitivity based on the sigma factor competition. Our theoretical analysis thus provides support for a significant role of passive control during that global switch of the gene expression program.

Bacteria respond to changing environmental conditions by switching the global pattern of expressed genes. A key mechanism for global switches of the transcriptional program depends on alternative sigma factors that bind the RNA polymerase core enzyme and direct it towards the appropriate stress response genes. Competition of different sigma factors for a limited amount of RNA polymerase is believed to play a central role in this global switch. Here, a theoretical approach is used towards a quantitative understanding of sigma factor competition and its effects on gene expression. The model is used to quantitatively describe in vitro competition assays and to address the question of indirect or passive control in the stringent response upon amino acids starvation. We show that sigma factor competition provides a mechanism for a passive up-regulation of the stress specific sigma-driven genes due to the increased availability of RNA polymerase in the stringent response. Moreover, we find that active separation of sigma factor from the RNA polymerase during early transcript elongation weakens the sigma factor-RNA polymerase equilibrium constant, raising the question of how their in vitro measure is relevant in the cell.

Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies

Recognition of bacterial promoters is regulated by two distinct classes of sequence-specific sigma factors, σ⁷⁰ or σ⁵⁴, that differ both in their primary sequence and in the requirement of the latter for activation via enhancer-bound upstream activators. The σ⁵⁴ version controls gene expression in response to stress, often mediating pathogenicity. Its activator proteins are members of the AAA+ superfamily and use adenosine triphosphate (ATP) hydrolysis to remodel initially auto-inhibited holoenzyme promoter complexes. We have mapped this remodeling using single-molecule fluorescence spectroscopy. Initial remodeling is nucleotide-independent and driven by binding both ssDNA during promoter melting and activator. However, DNA loading into the RNA polymerase active site depends on co-operative ATP hydrolysis by the activator. Although the coupled promoter recognition and melting steps may be conserved between σ⁷⁰ and σ⁵⁴, the domain movements of the latter have evolved to require an activator ATPase.

CRP-cyclic AMP dependent inhibition of the xylene-responsive σ(54)-promoter Pu in Escherichia coli

The expression of σ(54)-dependent Pseudomonas putida Pu promoter is activated by XylR activator when cells are exposed to a variety of aromatic inducers. In this study, the transcriptional activation of the P. putida Pu promoter was recreated in the heterologous host Escherichia coli. Here we show that the cAMP receptor protein (CRP), a well-known carbon utilization regulator, had an inhibitory effect on the expression of Pu promoter in a cAMP-dependent manner. The inhibitory effect was not activator specific. In vivo KMnO4 and DMS footprinting analysis indicated that CRP-cAMP poised the RNA polymerase at Pu promoter, inhibiting the isomerization step of the transcription initiation even in the presence of an activator. Therefore, the presence of PTS-sugar, which eliminates cAMP, could activate the poised RNA polymerase at Pu promoter to transcribe. Moreover, the activation region 1 (AR1) of CRP, which interacts directly with the αCTD (C-terminal domain of α-subunit) of RNA polymerase, was found essential for the CRP-mediated inhibition at Pu promoter. A model for the above observations is discussed.

Determination of the self-association residues within a homomeric and a heteromeric AAA+ enhancer binding protein

The σ(54)-dependent transcription in bacteria requires specific activator proteins, bacterial enhancer binding protein (bEBP), members of the AAA+ (ATPases Associated with various cellular Activities) protein family. The bEBPs usually form oligomers in order to hydrolyze ATP and make open promoter complexes. The bEBP formed by HrpR and HrpS activates transcription from the σ(54)-dependent hrpL promoter responsible for triggering the Type Three Secretion System in Pseudomonas syringae pathovars. Unlike other bEBPs that usually act as homohexamers, HrpR and HrpS operate as a highly co-dependent heterohexameric complex. To understand the organization of the HrpRS complex and the HrpR and HrpS strict co-dependence, we have analyzed the interface between subunits using the random and directed mutagenesis and available crystal structures of several closely related bEBPs. We identified key residues required for the self-association of HrpR (D32, E202 and K235) with HrpS (D32, E200 and K233), showed that the HrpR D32 and HrpS K233 residues form interacting pairs directly involved in an HrpR-HrpS association and that the change in side-chain length at position 233 in HrpS affects self-association and interaction with the HrpR and demonstrated that the HrpS D32, E200 and K233 are not involved in negative regulation imposed by HrpV. We established that the equivalent residues K30, E200 and E234 in a homo-oligomeric bEBP, PspF, are required for the subunit communication and formation of an oligomeric lock that cooperates with the ATP γ-phosphate sensing PspF residue R227, providing insights into their roles in the heteromeric HrpRS co-complex.

Structure, function, and tethering of DNA-binding domains in σ⁵⁴ transcriptional activators

We compare the structure, activity, and linkage of DNA-binding domains (DBDs) from σ(54) transcriptional activators and discuss how the properties of the DBDs and the linker to the neighboring domain are affected by the overall properties and requirements of the full proteins. These transcriptional activators bind upstream of specific promoters that utilize σ(54)-polymerase. Upon receiving a signal the activators assemble into hexamers, which then, through adenosine triphosphate (ATP) hydrolysis, drive a conformational change in polymerase that enables transcription initiation. We present structures of the DBDs of activators nitrogen regulatory protein C 1 (NtrC1) and Nif-like homolog 2 (Nlh2) from the thermophile Aquifex aeolicus. The structures of these domains and their relationship to other parts of the activators are discussed. These structures are compared with previously determined structures of the DBDs of NtrC4, NtrC, ZraR, and factor for inversion stimulation. The N-terminal linkers that connect the DBDs to the central domains in NtrC1 and Nlh2 were studied and found to be unstructured. Additionally, a crystal structure of full-length NtrC1 was solved, but density of the DBDs was extremely weak, further indicating that the linker between ATPase and DBDs functions as a flexible tether. Flexible linking of ATPase and DBDs is likely necessary to allow assembly of the active hexameric ATPase ring. The comparison of this set of activators also shows clearly that strong dimerization of the DBD only occurs when other domains do not dimerize strongly.

Divergent control of two type VI secretion systems by RpoN in Pseudomonas aeruginosa

Three Type VI Secretion System (T6SS) loci called H1- to H3-T6SS coexist in Pseudomonas aeruginosa. H1-T6SS targets prokaryotic cells whereas H2-T6SS mediates interactions with both eukaryotic and prokaryotic host cells. Little is known about the third system, except that it may be connected to H2-T6SS during the host infection. Here we show that H3-T6SS is required for P. aeruginosa PAO1 virulence in the worm model. We demonstrate that the two putative H3-T6SS operons, called "left" and "right", are coregulated with H2-T6SS by the Las and Rhl Quorum Sensing systems. Interestingly, the RpoN σ54 factor has divergent effects on the three operons. As for many T6SSs, RpoN activates the expression of H3-T6SS left. However, RpoN unexpectedly represses the expression of H3-T6SS right and also H2-T6SS. Sfa2 and Sfa3 are putative enhancer binding proteins encoded on H2-T6SS and H3-T6SS left. In other T6SSs EBPs can act as σ54 activators to promote T6SS transcription. Strikingly, we found that the RpoN effects of H3-T6SS are Sfa-independent while the RpoN mediated repression of H2-T6SS is Sfa2-dependent. This is the first example of RpoN repression of a T6SS being mediated by a T6SS-encoded EBP.

Expanding the boolean logic of the prokaryotic transcription factor XylR by functionalization of permissive sites with a protease-target sequence

The σ54-dependent prokaryotic regulator XylR implements a one-input/one-output actuator that transduces the presence of the aromatic effector m-xylene into transcriptional activation of the cognate promoter Pu. Such a signal conversion involves the effector-mediated release of the intramolecular repression of the N-terminal A domain on the central C module of XylR. On this background, we set out to endow this regulator with additional signal-sensing capabilities by inserting a target site of the viral protease NIa in permissive protein locations that once cleaved in vivo could either terminate XylR activity or generate an effector-independent, constitutive transcription factor. To find optimal protein positions to this end, we saturated the xylR gene DNA with a synthetic transposable element designed for randomly delivering in-frame polypeptides throughout the sequence of any given protein. This Tn5-based system supplies the target gene with insertions of a selectable marker that can later be excised, leaving behind the desired (poly) peptides grafted into the protein structure. Implementation of such knock-in-leave-behind (KILB) method to XylR was instrumental to produce a number of variants of this transcription factor (TF) that could compute in vivo two inputs (m-xylene and protease) into a single output following a logic that was dependent on the site of the insertion of the NIa target sequence in the TF. Such NIa-sensitive XylR specimens afforded the design of novel regulatory nodes that entered protease expression as one of the signals recognized in vivo for controlling Pu. This approach is bound to facilitate the functionalization of TFs and other proteins with new traits, especially when their forward engineering is made difficult by, for example, the absence of structural data.

Salmonella utilizes D-glucosaminate via a mannose family phosphotransferase system permease and associated enzymes

Salmonella enterica is a globally significant bacterial food-borne pathogen that utilizes a variety of carbon sources. We report here that Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) uses d-glucosaminate (2-amino-2-deoxy-d-gluconic acid) as a carbon and nitrogen source via a previously uncharacterized mannose family phosphotransferase system (PTS) permease, and we designate the genes encoding the permease dgaABCD (d-glucosaminate PTS permease components EIIA, EIIB, EIIC, and EIID). Two other genes in the dga operon (dgaE and dgaF) were required for wild-type growth of S. Typhimurium with d-glucosaminate. Transcription of dgaABCDEF was dependent on RpoN (σ(54)) and an RpoN-dependent activator gene we designate dgaR. Introduction of a plasmid bearing dgaABCDEF under the control of the lac promoter into Escherichia coli strains DH5α, BL21, and JM101 allowed these strains to grow on minimal medium containing d-glucosaminate as the sole carbon and nitrogen source. Biochemical and genetic data support a catabolic pathway in which d-glucosaminate, as it is transported across the cell membrane, is phosphorylated at the C-6 position by DgaABCD. DgaE converts the resulting d-glucosaminate-6-phosphate to 2-keto-3-deoxygluconate 6-phosphate (KDGP), which is subsequently cleaved by the aldolase DgaF to form glyceraldehyde-3-phosphate and pyruvate. DgaF catalyzes the same reaction as that catalyzed by Eda, a KDGP aldolase in the Entner-Doudoroff pathway, and the two enzymes can substitute for each other in their respective pathways. Examination of the Integrated Microbial Genomes database revealed that orthologs of the dga genes are largely restricted to certain enteric bacteria and a few species in the phylum Firmicutes.

An aromatic residue switch in enhancer-dependent bacterial RNA polymerase controls transcription intermediate complex activity

The formation of the open promoter complex (RPo) in which the melted DNA containing the transcription start site is located at the RNA polymerase (RNAP) catalytic centre is an obligatory step in the transcription of DNA into RNA catalyzed by RNAP. In the RPo, an extensive network of interactions is established between DNA, RNAP and the σ-factor and the formation of functional RPo occurs via a series of transcriptional intermediates (collectively 'RPi'). A single tryptophan is ideally positioned to directly engage with the flipped out base of the non-template strand at the +1 site. Evidence suggests that this tryptophan (i) is involved in either forward translocation or DNA scrunching and (ii) in σ(54)-regulated promoters limits the transcription activity of at least one intermediate complex (RPi) before the formation of a fully functional RPo. Limiting RPi activity may be important in preventing the premature synthesis of abortive transcripts, suggesting its involvement in a general mechanism driving the RPi to RPo transition for transcription initiation.

The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription

Bacterial enhancer binding proteins (bEBPs) are transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ(54). We present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. The review is structured by introducing each of the three domains in turn: the central catalytic domain, the N-terminal regulatory domain, and the C-terminal DNA binding domain. The role of the central catalytic domain is presented with particular reference to (i) oligomerization, (ii) ATP hydrolysis, and (iii) the key GAFTGA motif that contacts σ(54) for remodeling. Each of these functions forms a potential target of the signal-sensing N-terminal regulatory domain, which can act either positively or negatively to control the activation of σ(54)-dependent transcription. Finally, we focus on the DNA binding function of the C-terminal domain and the enhancer sites to which it binds. Particular attention is paid to the importance of σ(54) to the bacterial cell and its unique role in regulating transcription.

A dual switch controls bacterial enhancer-dependent transcription

Bacterial RNA polymerases (RNAPs) are targets for antibiotics. Myxopyronin binds to the RNAP switch regions to block structural rearrangements needed for formation of open promoter complexes. Bacterial RNAPs containing the major variant σ(54) factor are activated by enhancer-binding proteins (bEBPs) and transcribe genes whose products are needed in pathogenicity and stress responses. We show that (i) enhancer-dependent RNAPs help Escherichia coli to survive in the presence of myxopyronin, (ii) enhancer-dependent RNAPs partially resist inhibition by myxopyronin and (iii) ATP hydrolysis catalysed by bEBPs is obligatory for functional interaction of the RNAP switch regions with the transcription start site. We demonstrate that enhancer-dependent promoters contain two barriers to full DNA opening, allowing tight regulation of transcription initiation. bEBPs engage in a dual switch to (i) allow propagation of nucleated DNA melting from an upstream DNA fork junction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at the RNA synthesis start site, resulting in switch region-dependent RNAP clamp closure and open promoter complex formation.

ATPase site architecture is required for self-assembly and remodeling activity of a hexameric AAA+ transcriptional activator

AAA+ proteins (ATPases associated with various cellular activities) are oligomeric ATPases that use ATP hydrolysis to remodel their substrates. By similarity with GTPases, a dynamic organization of the nucleotide-binding pockets between ATPase protomers is proposed to regulate functionality. Using the transcription activator PspF as an AAA+ model, we investigated contributions of conserved residues for roles in ATP hydrolysis and intersubunit communication. We determined the R-finger residue and revealed that it resides in a conserved “R-hand” motif (R_xD_xxxR) needed for its “trans-acting” activity. Further, a divergent Walker A glutamic acid residue acts synergistically with a tyrosine residue to function in ADP-dependent subunit-subunit coordination, forming the “ADP-switch” motif. Another glutamic acid controls hexamer formation in the presence of nucleotides. Together, these results lead to a “residue-nucleotide” interaction map upon which to base AAA+ core regulation.

Towards synthetic gene circuits with enhancers: biology's multi-input integrators

One of the greatest challenges facing synthetic biology is to develop a technology that allows gene regulatory circuits in microbes to integrate multiple inputs or stimuli using a small DNA sequence "foot-print", and which will generate precise and reproducible outcomes. Achieving this goal is hindered by the routine utilization of the commonplace σ(70) promoters in gene-regulatory circuits. These promoters typically are not capable of integrating binding of more than two or three transcription factors in natural examples, which has limited the field to developing integrated circuits made of two-input biological "logic" gates. In natural examples the regulatory elements, which integrate multiple inputs are called enhancers. These regulatory elements are ubiquitous in all organisms in the tree of life, and interestingly metazoan and bacterial enhancers are significantly more similar in terms of both Transcription Factor binding site arrangement and biological function than previously thought. These similarities imply that there may be underlying enhancer design principles or grammar rules by which one can engineer novel gene regulatory circuits. However, at present our current understanding of enhancer structure-function relationship in all organisms is limited, thus preventing us from using these objects routinely in synthetic biology application. In order to alleviate this problem, in this book chapter, I will review our current view of bacterial enhancers, allowing us to first highlight the potential of enhancers to be a game-changing tool in synthetic biology application, and subsequently to draw a road-map for developing the necessary quantitative understanding to reach this goal.

Insights from the architecture of the bacterial transcription apparatus

We provide a portrait of the bacterial transcription apparatus in light of the data emerging from structural studies, sequence analysis and comparative genomics to bring out important but underappreciated features. We first describe the key structural highlights and evolutionary implications emerging from comparison of the cellular RNA polymerase subunits with the RNA-dependent RNA polymerase involved in RNAi in eukaryotes and their homologs from newly identified bacterial selfish elements. We describe some previously unnoticed domains and the possible evolutionary stages leading to the RNA polymerases of extant life forms. We then present the case for the ancient orthology of the basal transcription factors, the sigma factor and TFIIB, in the bacterial and the archaeo-eukaryotic lineages. We also present a synopsis of the structural and architectural taxonomy of specific transcription factors and their genome-scale demography. In this context, we present certain notable deviations from the otherwise invariant proteome-wide trends in transcription factor distribution and use it to predict the presence of an unusual lineage-specifically expanded signaling system in certain firmicutes like Paenibacillus. We then discuss the intersection between functional properties of transcription factors and the organization of transcriptional networks. Finally, we present some of the interesting evolutionary conundrums posed by our newly gained understanding of the bacterial transcription apparatus and potential areas for future explorations.

Coupling AAA protein function to regulated gene expression

AAA proteins (ATPases Associated with various cellular Activities) are involved in almost all essential cellular processes ranging from DNA replication, transcription regulation to protein degradation. One class of AAA proteins has evolved to adapt to the specific task of coupling ATPase activity to activating transcription. These upstream promoter DNA bound AAA activator proteins contact their target substrate, the σ(54)-RNA polymerase holoenzyme, through DNA looping, reminiscent of the eukaryotic enhance binding proteins. These specialised macromolecular machines remodel their substrates through ATP hydrolysis that ultimately leads to transcriptional activation. We will discuss how AAA proteins are specialised for this specific task.

Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification

A flavorubredoxin and its associated oxidoreductase (encoded by norV and norW respectively) detoxify NO (nitric oxide) to form N2O (nitrous oxide) under anaerobic conditions in Escherichia coli. Transcription of the norVW genes is activated in response to NO by the σ54-dependent regulator and dedicated NO sensor, NorR, a member of the bacterial enhancer-binding protein family. In the absence of NO, the catalytic activity of the central ATPase domain of NorR is repressed by the N-terminal regulatory domain that contains a non-haem iron centre. Binding of NO to this centre results in the formation of a mononitrosyl iron species, enabling the activation of ATPase activity. Our studies suggest that the highly conserved GAFTGA loop in the ATPase domain, which engages with the alternative σ factor σ54 to activate transcription, is a target for intramolecular repression by the regulatory domain. Binding of NorR to three conserved enhancer sites upstream of the norVW promoter is essential for transcriptional activation and promotes the formation of a stable higher-order NorR nucleoprotein complex. We propose that enhancer-driven assembly of this oligomeric complex, in which NorR apparently forms a DNA-bound hexamer in the absence of NO, provides a 'poised' system for transcriptional activation that can respond rapidly to nitrosative stress.

Regulation of type VI secretion gene clusters by sigma54 and cognate enhancer binding proteins

Type VI secretion systems (T6SS) are bacteriophage-derived macromolecular machines responsible for the release of at least two proteins in the milieu, which are thought to form an extracellular appendage. Although several T6SS have been shown to be involved in the virulence of animal and plant pathogens, clusters encoding these machines are found in the genomes of most species of gram-negative bacteria, including soil, marine, and environmental isolates. T6SS have been associated with several phenotypes, ranging from virulence to biofilm formation or stress sensing. Their various environmental niches and large diversity of functions are correlated with their broad variety of regulatory mechanisms. Using a bioinformatic approach, we identified several clusters, including those of Vibrio cholerae, Aeromonas hydrophila, Pectobacterium atrosepticum, Pseudomonas aeruginosa, Pseudomonas syringae pv. tomato, and a Marinomonas sp., which possess typical -24/-12 sequences, recognized by the alternate sigma factor sigma 54 (σ(54) or σ(N)). σ(54), which directs the RNA polymerase to these promoters, requires the action of a bacterial enhancer binding protein (bEBP), which binds to cis-acting upstream activating sequences. Putative bEBPs are encoded within the T6SS gene clusters possessing σ(54) boxes. Using in vitro binding experiments and in vivo reporter fusion assays, we showed that the expression of these clusters is dependent on both σ(54) and bEBPs.

Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR

Bacterial enhancer binding proteins (bEBPs) are specialized transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ⁵⁴. Transcriptional activation by the NorR bEBP is controlled by a regulatory GAF domain that represses the ATPase activity of the central AAA+ domain in the absence of nitric oxide. Here, we investigate the mechanism of interdomain repression in NorR by characterizing substitutions in the AAA+ domain that bypass repression by the regulatory domain. Most of these substitutions are located in the vicinity of the surface-exposed loops that engage σ⁵⁴ during the ATP hydrolysis cycle or in the highly conserved GAFTGA motif that directly contacts σ⁵⁴. Biochemical studies suggest that the bypass mutations in the GAFTGA loop do not influence the DNA binding properties of NorR or the assembly of higher order oligomers in the presence of enhancer DNA, and as expected these variants retain the ability to activate open complex formation in vitro. We identify a crucial arginine residue in the GAF domain that is essential for interdomain repression and demonstrate that hydrophobic substitutions at this position suppress the bypass phenotype of the GAFTGA substitutions. These observations suggest a novel mechanism for negative regulation in bEBPs in which the GAF domain targets the σ⁵⁴-interaction surface to prevent access of the AAA+ domain to the sigma factor.

Single chain forms of the enhancer binding protein PspF provide insights into geometric requirements for gene activation

Genetic information in the DNA is accessed by the molecular machine RNA polymerase following a highly conserved process, invariably involving the transition between double-stranded and single-stranded DNA states. In the case of the bacterial enhancer-dependent RNA polymerase (which is essential for adaptive responses and bacterial pathogenesis), the DNA melting event depends on specialized hexameric AAA+ ATPase activators. Involvement of such factors in transcription was demonstrated 25 years ago, but why these activators need to be hexameric, whether all the subunits operate identically, what is the contribution of each of the six subunits within the hexamer (structural, functional, or both), and how many active subunits are required for transcription activation remain open questions. Using engineered single-chain polypeptides covalently linking two or three subunits of the activator (allowing the subunit distribution within a hexamer to be fixed), we now show that (i) individual subunits have differential contributions to the activities of the oligomer and (ii) only a fraction of the subunits within the hexameric ATPase is directly required for gene activation. We establish that nucleotide-dependent coordination across three subunits of the hexameric bacterial enhancer binding proteins (bEBPs) is necessary for engagement and remodeling of the closed complex (RPc). Outcomes revealed features of bEBP, distinguishing their mode of action from fully processive AAA+ proteins or from simple bimodal switches. We now propose that the hexamer functions with asymmetric organization, potentially involving a split planar (open ring) or spiral character.

Regulation of glutamate dehydrogenase expression in Pseudomonas putida results from its direct repression by NtrC under nitrogen-limiting conditions

Nitrogen-regulated genes in enterobacteria are positively controlled by the transcriptional activator of σ(N) -dependent promoters NtrC, either directly or indirectly, through the dual regulator Nac. Similar to enterobacteria, gdhA encoding glutamate dehydrogenase from Pseudomonas putida is one of the few genes that is induced by excess nitrogen. In P. putida, the binding of NtrC to the gdhA promoter region and in vitro transcription suggest that, unlike its enterobacterial homologue that is repressed by Nac, gdhA is directly repressed by NtrC. Footprinting analyses demonstrated that NtrC binds to four distinct sites in the gdhA promoter. NtrC dimers bind cooperatively, and those bound closer to the promoter interact with the dimers bound further upstream, thus producing a proposed repressor loop in the DNA. The formation of the higher-order complex and the repressor loop appears to be important for repression but not absolutely essential. Both the phosphorylated and the non-phosphorylated forms of NtrC efficiently repressed gdhA transcription in vitro and in vivo. Therefore, NtrC repression of gdhA under nitrogen-limiting conditions does not depend on the phosphorylation of the regulator; rather, it relies on an increase in the repressor concentration under these conditions.

Dimerization of the AtoC response regulator and modelling of its binding to DNA

Bacterial signal transduction systems can be viewed as an entity of multi-sensory and output domains, whereas the functions of response regulators play a pivotal role in the complex network interactions. One crucial property among response regulators functions is their oligomerization and subsequent binding to DNA. The AtoS-AtoC two component system, functionally modulated by various agents, influences fundamental cellular processes such as short-chain fatty acid catabolism and poly-(R)-3-hydroxybutyrate biosynthesis in Escherichia coli. Among the already reported characteristic properties, AtoC binds to a specific site, a palindromic repeat of 20 nucleotides within the atoDAEB promoter. Since experimental structures of AtoC or its complex with DNA are not yet available, an almost complete homology model of AtoC and of its putative entity as a dimer is constructed for this study, as well as a model of its binding to its target DNA sequence. The latter is associated with large conformational changes, as shown by molecular dynamics simulations. Subsequent biochemical study, including cross-linking via chemical agents, revealed the ability of AtoC to form oligomers in vitro.

Evidence for amino acid roles in the chemistry of ATP hydrolysis in Escherichia coli Rho

Many proteins that hydrolyze ATP or GTP have comparable amino acid residues for which specific roles have been proposed in a mechanism for the chemistry of hydrolysis. These roles include polarization by a glutamate residue of a water molecule for the attack on the γ-phosphoryl group of the nucleotide, stabilization of the transition state by an arginine finger, discrimination between bound nucleoside triphosphate and diphosphate by a γ sensor residue, and coordination by an aspartate of the Mg(2+) that accompanies the substrate nucleotide. We mutated four candidate residues for these roles in the Escherichia coli transcription termination factor Rho, E211, R366, R212, and D265, and characterized the resulting proteins for oligomerization state, ligand binding, RNA-dependent ATP hydrolysis, and, in rapid mix/chemical quench experiments, achievement of the chemistry step of hydrolysis. All four mutant proteins behaved as expected for Rhos lacking the proposed mechanistic roles. The results provide firm biochemical evidence in support of the proposed model for hydrolysis chemistry.

Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology

The bacterial phage shock protein (Psp) response functions to help cells manage the impacts of agents impairing cell membrane function. The system has relevance to biotechnology and to medicine. Originally discovered in Escherichia coli, Psp proteins and homologues are found in Gram-positive and Gram-negative bacteria, in archaea and in plants. Study of the E. coli and Yersinia enterocolitica Psp systems provides insights into how membrane-associated sensory Psp proteins might perceive membrane stress, signal to the transcription apparatus and use an ATP-hydrolysing transcription activator to produce effector proteins to overcome the stress. Progress in understanding the mechanism of signal transduction by the membrane-bound Psp proteins, regulation of the psp gene-specific transcription activator and the cell biology of the system is presented and discussed. Many features of the action of the Psp system appear to be dominated by states of self-association of the master effector, PspA, and the transcription activator, PspF, alongside a signalling pathway that displays strong conditionality in its requirement.

Mechanisms for activating bacterial RNA polymerase

Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP) enzymes and is highly regulated through the action of gene regulatory complexes. Important mechanistic insights have been gained from structural studies on multisubunit RNAP from bacteria, yeast and archaea, although the initiation process that involves the conversion of the inactive transcription complex to an active one has yet to be fully understood. RNAPs are unambiguously closely related in structure and function across all kingdoms of life and have conserved mechanisms. In bacteria, sigma (sigma) factors direct RNAP to specific promoter sites and the RNAP/sigma holoenzyme can either form a stable closed complex that is incompetent for transcription (as in the case of sigma(54)) or can spontaneously proceed to an open complex that is competent for transcription (as in the case of sigma(70)). The conversion of the RNAP/sigma(54) closed complex to an open complex requires ATP hydrolysis by enhancer-binding proteins, hence providing an ideal model system for studying the initiation process biochemically and structurally. In this review, we present recent structural studies of the two major bacterial RNAP holoenzymes and focus on mechanistic advances in the transcription initiation process via enhancer-binding proteins.

Engineered interfaces of an AAA+ ATPase reveal a new nucleotide-dependent coordination mechanism

Homohexameric ring AAA(+) ATPases are found in all kingdoms of life and are involved in all cellular processes. To accommodate the large spectrum of substrates, the conserved AAA(+) core has become specialized through the insertion of specific substrate-binding motifs. Given their critical roles in cellular function, understanding the nucleotide-driven mechanisms of action is of wide importance. For one type of member AAA(+) protein (phage shock protein F, PspF), we identified and established the functional significance of strategically placed arginine and glutamate residues that form interacting pairs in response to nucleotide binding. We show that these interactions are critical for "cis" and "trans" subunit communication, which support coordination between subunits for nucleotide-dependent substrate remodeling. Using an allele-specific suppression approach for ATPase and substrate remodeling, we demonstrate that the targeted residues directly interact and are unlikely to make any other pairwise critical interactions. We then propose a mechanistic rationale by which the nucleotide-bound state of adjacent subunits can be sensed without direct involvement of R-finger residues. As the structural AAA(+) core is conserved, we propose that the functional networks established here could serve as a template to identify similar residue pairs in other AAA(+) proteins.

Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

BACKGROUND

Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism.

RESULTS

In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (sigma54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 sigma54-dependent promoter motif was identified upstream of aoxAB coding sequences.

CONCLUSION

These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.

Involvement of MmoR and MmoG in the transcriptional activation of soluble methane monooxygenase genes in Methylosinus trichosporium OB3b

Methanotrophs oxidize methane to methanol using the enzyme methane monooxygenase. Methylosinus trichosporium OB3b has two such enzymes: a membrane-bound particulate methane monooxygenase (pMMO) and a soluble, cytoplasmic methane monooxygenase (sMMO). In methanotrophs possessing both enzymes, the expression of the genes encoding sMMO and pMMO is regulated by copper ions, with sMMO expressed solely when copper is limiting. Virtually nothing is known about the specific machinery involved in the copper-regulated transcription of mmo genes except the identification of two proteins necessary for the expression: a sigma(54)-dependent transcriptional activator, MmoR, and a putative GroEL-like chaperone, MmoG. Genes encoding mmoR and mmoG are located immediately upstream of those encoding sMMO in the genome of M. trichosporium OB3b. Here, we use a green fluorescent protein promoter probe vector to show that nearly the complete intergenic DNA sequence between mmoG and mmoX is absolutely required for transcriptional activation. Furthermore, we used gel-shift assays to demonstrate that both MmoR and MmoG were required for protein binding to this region of DNA.

A lower-order oligomer form of phage shock protein A (PspA) stably associates with the hexameric AAA(+) transcription activator protein PspF for negative regulation

To survive and colonise their various environments, including those used during infection, bacteria have developed a variety of adaptive systems. Amongst these is phage shock protein (Psp) response, which can be induced in Escherichia coli upon filamentous phage infection (specifically phage secretin pIV) and by other membrane-damaging agents. The E. coli Psp system comprises seven proteins, of which PspA is the central component. PspA is a bifunctional protein that is directly involved in (i) the negative regulation of the psp-specific transcriptional activator PspF and (ii) the maintenance of membrane integrity in a mechanism proposed to involve the formation of a 36-mer ring complex. Here we established that the PspA negative regulation of PspF ATPase activity is the result of a cooperative inhibition. We present biochemical evidence showing that an inhibitory PspA–PspF regulatory complex, which has significantly reduced PspF ATPase activity, is composed of around six PspF subunits and six PspA subunits, suggesting that PspA exists in at least two different oligomeric assemblies. We now establish that all four putative helical domains of PspA are critical for the formation of the 36-mer. In contrast, not all four helical domains are required for the formation of the inhibitory PspA–PspF complex. Since a range of initial PspF oligomeric states permit formation of the apparent PspA–PspF dodecameric assembly, we conclude that PspA and PspF demonstrate a strong propensity to self-assemble into a single defined heteromeric regulatory complex.

NtrC-dependent regulatory network for nitrogen assimilation in Pseudomonas putida

Pseudomonas putida KT2440 is a model strain for studying bacterial biodegradation processes. However, very little is known about nitrogen regulation in this strain. Here, we show that the nitrogen regulatory NtrC proteins from P. putida and Escherichia coli are functionally equivalent and that substitutions leading to partially active forms of enterobacterial NtrC provoke the same phenotypes in P. putida NtrC. P. putida has only a single P(II)-like protein, encoded by glnK, whose expression is nitrogen regulated. Two contiguous NtrC binding sites located upstream of the sigma(N)-dependent glnK promoter have been identified by footprinting analysis. In vitro experiments with purified proteins demonstrated that glnK transcription was directly activated by NtrC and that open complex formation at this promoter required integration host factor. Transcription of genes orthologous to enterobacterial codB, dppA, and ureD genes, whose transcription is dependent on sigma(70) and which are activated by Nac in E. coli, has also been analyzed for P. putida. Whereas dppA does not appear to be regulated by nitrogen via NtrC, the codB and ureD genes have sigma(N)-dependent promoters and their nitrogen regulation was exerted directly by NtrC, thus avoiding the need for Nac, which is missing in this bacterial species. Based upon these results, we propose a simplified nitrogen regulatory network in P. putida (compared to that in enterobacteria), which involves an indirect-feedback autoregulation of glnK using NtrC as an intermediary.

Activation and repression of a sigmaN-dependent promoter naturally lacking upstream activation sequences

The Pseudomonas sp. strain ADP protein AtzR is a LysR-type transcriptional regulator required for activation of the atzDEF operon in response to nitrogen limitation and cyanuric acid. Transcription of atzR is directed by the sigma(N)-dependent promoter PatzR, activated by NtrC and repressed by AtzR. Here we use in vivo and in vitro approaches to address the mechanisms of PatzR activation and repression. Activation by NtrC did not require any promoter sequences other than the sigma(N) recognition motif both in vivo and in vitro, suggesting that NtrC activates PatzR in an upstream activation sequences-independent fashion. Regarding AtzR-dependent autorepression, our in vitro transcription experiments show that the concentration of AtzR required for repression of the PatzR promoter in vitro correlates with AtzR affinity for its binding site. In addition, AtzR prevents transcription from PatzR when added to a preformed E-sigma(N)-PatzR closed complex, but isomerization to an open complex prevents repression. Gel mobility shift and DNase I footprint assays indicate that DNA-bound AtzR and E-sigma(N) are mutually exclusive. Taken together, these results strongly support the notion that AtzR represses transcription from PatzR by competing with E-sigma(N) for their overlapping binding sites. There are no previous reports of a similar mechanism for repression of sigma(N)-dependent transcription.

Comparative analysis of activator-Esigma54 complexes formed with nucleotide-metal fluoride analogues

Bacterial RNA polymerase (RNAP) containing the major variant σ⁵⁴ factor forms open promoter complexes in a reaction in which specialized activator proteins hydrolyse ATP. Here we probe binding interactions between σ⁵⁴-RNAP (Eσ⁵⁴) and the ATPases associated with various cellular activities (AAA+) domain of the Escherichia coli activator protein, PspF, using nucleotide-metal fluoride (BeF and AlF) analogues representing ground and transition states of ATP, which allow complexes (that are otherwise too transient with ATP) to be captured. We show that the organization and functionality of the ADP–BeF- and ADP–AlF-dependent complexes greatly overlap. Our data support an activation pathway in which the initial ATP-dependent binding of the activator to the Eσ⁵⁴ closed complex results in the re-organization of Eσ⁵⁴ with respect to the transcription start-site. However, the nucleotide-dependent binding interactions between the activator and the Eσ⁵⁴ closed complex are in themselves insufficient for forming open promoter complexes when linear double-stranded DNA is present in the initial closed complex.

Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein

Molecular machines belonging to the AAA+ superfamily of ATPases use NTP hydrolysis to remodel their versatile substrates. The presence of an insertion sequence defines the major phylogenetic pre-sensor I insertion (pre-SIi) AAA+ superclade. In the bacterial σ⁵⁴-dependent enhancer binding protein phage shock protein F (PspF) the pre-SIi loop adopts different conformations depending on the nucleotide-bound state. Single amino acid substitutions within the dynamic pre-SIi loop of PspF drastically change the ATP hydrolysis parameters, indicating a structural link to the distant hydrolysis site. We used a site-specific protein–DNA proximity assay to measure the contribution of the pre-SIi loop in σ⁵⁴-dependent transcription and demonstrate that the pre-SIi loop is a major structural feature mediating nucleotide state-dependent differential engagement with Eσ⁵⁴. We suggest that much, if not all, of the action of the pre-SIi loop is mediated through the L1 loop and relies on a conserved molecular switch, identified in a crystal structure of one pre-SIi variant and in accordance with the high covariance between some pre-SIi residues and distinct residues outside the pre-SIi sequence.

Identification of the binding site of the σ 54 hetero-oligomeric FleQ/FleT activator in the flagellar promoters of Rhodobacter sphaeroides

Expression of the flagellar genes in Rhodobacter sphaeroides is dependent on one of the four sigma-54 factors present in this bacterium and on the enhancer binding proteins (EBPs) FleQ and FleT. These proteins, in contrast to other well-characterized EBPs, carry out activation as a hetero-oligomeric complex. To further characterize the molecular properties of this complex we mapped the binding sites or upstream activation sequences (UASs) of six different flagellar promoters. In most cases the UASs were identified at approximately 100 bp upstream from the promoter. However, the activity of the divergent promoters flhAp-flgAp, which are separated by only 53 bp, is mainly dependent on a UAS located approximately 200 bp downstream from each promoter. Interestingly, a significant amount of activation mediated by the upstream or contralateral UAS was also detected, suggesting that the architecture of this region is important for the correct regulation of these promoters. Sequence analysis of the regions carrying the potential FleQ/FleT binding sites revealed a conserved motif. In vivo footprinting experiments with the motAp promoter allowed us to identify a protected region that overlaps with this motif. These results allow us to propose a consensus sequence that represents the binding site of the FleQ/FleT activating complex.

Iron-based redox switches in biology

By virtue of its unique electrochemical properties, iron makes an ideal redox active cofactor for many biologic processes. In addition to its important role in respiration, central metabolism, nitrogen fixation, and photosynthesis, iron also is used as a sensor of cellular redox status. Iron-based sensors incorporate Fe-S clusters, heme, and mononuclear iron sites to act as switches to control protein activity in response to changes in cellular redox balance. Here we provide an overview of iron-based redox sensor proteins, in both prokaryotes and eukaryotes, that have been characterized at the biochemical level. Although this review emphasizes redox sensors containing Fe-S clusters, proteins that use heme or novel iron sites also are discussed.

IHF-binding sites inhibit DNA loop formation and transcription initiation

Transcriptional activation of enhancer and σ⁵⁴-dependent promoters requires efficient interactions between enhancer-binding proteins (EBP) and promoter bound σ⁵⁴-RNA polymerase (Eσ⁵⁴) achieved by DNA looping, which is usually facilitated by the integration host factor (IHF). Since the lengths of the intervening region supporting DNA-loop formation are similar among IHF-dependent and IHF-independent promoters, the precise reason(s) why IHF is selectively important for the frequency of transcription initiation remain unclear. Here, using kinetic cyclization and in vitro transcription assays we show that, in the absence of IHF protein, the DNA fragments containing an IHF-binding site have much less looping-formation ability than those that lack an IHF-binding site. Furthermore, when an IHF consensus-binding site was introduced into the intervening region between promoter and enhancer of the target DNA fragments, loop formation and DNA-loop-dependent transcriptional activation are significantly reduced in a position-independent manner. DNA-looping-independent transcriptional activation was unaffected. The binding of IHF to its consensus site in the target promoters clearly restored efficient DNA looping formation and looping-dependent transcriptional activation. Our data provide evidence that one function for the IHF protein is to release a communication block set by intrinsic properties of the IHF DNA-binding site.

Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma54-promoter Pu to the response regulator PprA

Implantation of the regulatory circuit of the degradation pathway of TOL plasmid pWW0 in the native transcriptional network of the host Pseudomonas putida involves interplay between plasmid- and chromosome-encoded factors. We have employed a reverse genetics approach to investigate such a molecular wiring by identifying host proteins that form stable complexes with Pu, the sigma(54)-dependent promoter of the upper TOL operon of pWW0. This approach revealed that the Pu upstream activating sequences (UAS), the target sites of the cognate activator XylR, form a specific complex with a host protein which, following DNA affinity purification and mass spectrometry analysis, was identified as the LytTR-type two-component response regulator PprA. Directed inactivation of pprA resulted in the upregulation of the Pu promoter in vivo, while expression of the same gene from a plasmid vector strongly repressed Pu activity. Such a downregulation of Pu by PprA could be faithfully reproduced both in vitro with purified components and in an in vivo reporter system assembled in Escherichia coli. The overlap of the PprA and XylR binding sites suggested that the basis for the inhibitory effect on Pu was a mutual exclusion mechanism between the two proteins to bind the UAS. We argue that the binding of the response regulator PprA to Pu (a case without precedents in sigma(54)-dependent transcription) helps to anchor the TOL regulatory subnetwork to the wider context of the host transcriptome, thereby allowing the entry of physiological signals that modulate the outcome of promoter activity.

Identification and functional characterization of NifA variants that are independent of GlnB activation in the photosynthetic bacterium Rhodospirillum rubrum

The activity of NifA, the transcriptional activator of the nitrogen fixation (nif) gene, is tightly regulated in response to ammonium and oxygen. However, the mechanisms for the regulation of NifA activity are quite different among various nitrogen-fixing bacteria. Unlike the well-studied NifL-NifA regulatory systems in Klebsiella pneumoniae and Azotobacter vinelandii, in Rhodospirillum rubrum NifA is activated by a direct protein-protein interaction with the uridylylated form of GlnB, which in turn causes a conformational change in NifA. We report the identification of several substitutions in the N-terminal GAF domain of R. rubrum NifA that allow NifA to be activated in the absence of GlnB. Presumably these substitutions cause conformational changes in NifA necessary for activation, without interaction with GlnB. We also found that wild-type NifA can be activated in a GlnB-independent manner under certain growth conditions, suggesting that some other effector(s) can also activate NifA. An attempt to use Tn5 mutagenesis to obtain mutants that altered the pool of these presumptive effector(s) failed, though much rarer spontaneous mutations in nifA were detected. This suggests that the necessary alteration of the pool of effector(s) for NifA activation cannot be obtained by knockout mutations.

Characterization of the nitric oxide-reactive transcriptional activator NorR

The prokaryotic transcriptional regulator NorR is unusual in that it utilizes a mononuclear ferrous iron center rather than a heme moiety as a means of sensing nitric oxide (NO). Binding of NO to the nonheme iron center in the amino-terminal GAF domain of NorR results in formation of a mononitrosyl iron complex and relieves intramolecular repression within NorR, allowing this regulatory protein, a member of the sigma(54)-dependent family of enhancer-binding proteins, to activate expression of genes required for NO detoxification. This chapter describes detailed protocols for measuring transcriptional activation by Escherichia coli NorR in vivo and in vitro. It also details spectroscopic methods for analysis of the interaction of NO with the nonheme iron center and determination of the NO-binding affinity constant.

Metal-containing sensor proteins sensing diatomic gas molecules

Diatomic gas molecules such as O2, CO and NO act as signaling molecules in many biological systems, where metal-containing gas sensor proteins sense their effector gas molecules by using prosthetic groups such as heme, iron-sulfur clusters and non-heme iron as the active center for gas sensing. When the gas sensor proteins sense their effector gas molecules, intramolecular and intermolecular signal transductions take place to regulate many physiological functions including gene expression, aerotaxis, and change in metabolic pathways, etc. The metal-containing prosthetic groups in these sensor proteins play a crucial role for selective sensing of their effectors. In this perspective, I will discuss the structure and function of some O2-, CO- and NO-sensor proteins, especially focussing on the structural, biochemical and biophysical properties of the active centers of these sensor proteins.

An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation

AAA+ proteins (ATPases associated with various cellular activities) contribute to many cellular processes and typically function as higher order oligomers permitting the coordination of nucleotide hydrolysis for functional output, which leads to substrate remodeling. The precise mechanisms that enable the relay of nucleotide hydrolysis to their specific functional outputs are largely unknown. Here we use PspF, a specialized AAA+ protein required for enhancer-dependent transcription activation in Escherichia coli, as a model system to address this question. We demonstrate that a conserved asparagine is involved in internal organization of the oligomeric ring, regulation of ATPase activity by "trans" factors, and optimizing substrate remodeling. We provide evidence that the spatial relationship between the asparagine residue and the Walker B motif is one key element in the conformational signaling pathway that leads to substrate remodeling. Such functional organization most likely applies to other AAA+ proteins, including Ltag (simian virus 40), Rep40 (Adeno-associated virus-2), and p97 (Mus musculus) in which the asparagine to Walker B motif relationship is conserved.

Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor

Bacterial sigma (sigma) factors confer gene specificity upon the RNA polymerase, the central enzyme that catalyses gene transcription. The binding of the alternative sigma factor sigma(54) confers upon the RNA polymerase special functional and regulatory properties, making it suited for control of several major adaptive responses. Here, we summarize our current understanding of the interactions the sigma(54) factor makes with the bacterial transcription machinery.

Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins

bEBPs (bacterial enhancer-binding proteins) are AAA+ (ATPase associated with various cellular activities) transcription activators that activate gene transcription through a specific bacterial sigma factor, sigma(54). Sigma(54)-RNAP (RNA polymerase) binds to promoter DNA sites and forms a stable closed complex, unable to proceed to transcription. The closed complex must be remodelled using energy from ATP hydrolysis provided by bEBPs to melt DNA and initiate transcription. Recently, large amounts of structural and biochemical data have produced insights into how ATP hydrolysis within the active site of bEBPs is coupled to the re-modelling of the closed complex. In the present article, we review some of the key nucleotides, mutations and techniques used and how they have contributed towards our understanding of the function of bEBPs.

Analysis of the nitric oxide-sensing non-heme iron center in the NorR regulatory protein

The NorR regulatory protein senses nitric oxide (NO) to activate genes required for NO detoxification under anaerobic and microaerobic conditions in Escherichia coli. NorR belongs to the sigma(54)-dependent family of transcriptional activators and contains an N-terminal regulatory GAF (cGMP phosphodiesterase, adenylate cyclase, FhlA) domain that controls the ATPase activity of the central AAA+ domain to regulate productive interactions with sigma(54). Binding of NO to a non-heme iron center in the GAF domain results in the formation of a mononitrosyl-iron complex and releases intramolecular repression of the AAA+ domain to enable activation of transcription. In this study, we have further characterized NorR spectroscopically and substituted conserved residues in the GAF domain. This analysis, in combination with structural modeling of the GAF domain, has identified five candidate ligands to the non-heme iron and suggests a model in which the metal ion is coordinated in a pseudo-octahedral environment by three aspartate residues, an arginine, and a cysteine.